[gmx-users] Re: gmx-users digest, Vol 1 #804 - 10 msgs

Regina R. Monaco, Ph.D. rocket at earthlight.com
Fri May 30 16:44:01 CEST 2003

	You are correct - the problem lies with the "UNK" residues. I 
hand-edited the residue names and GROMACS atom types into the .pdb 
obtained from PRODRG2 and pdb2gmx ran ok.

	I am starting this calculation with a .mol file, which does not have 
any residue information - just coordinates. I am not really fond of the 
idea of hand-editing these peptide files as a working solution, so does 
anyone know of a way I can take a .mol file and have some GROMACS or 
some other software recognize, or allow me to graphically edit, the 
residues and atom types?


    8. Re: Fwd: [gmx-users] D-form amino acids (Christoph Freudenberger)

Message: 8
Date: Fri, 30 May 2003 07:54:41 +0200
From: Christoph Freudenberger 
<christoph.freudenberger at chemie.uni-ulm.de>
Organization: University of Ulm
To: gmx-users at gromacs.org
Subject: Re: Fwd: [gmx-users] D-form amino acids
Reply-To: gmx-users at gromacs.org

Regina R. Monaco, Ph.D. wrote:
> Hi Daan-
>     Well, **I** am not worried, but GROMACS won't accept the
> calculation.  I am assuming the reason is that the program is not
> certain what the  atom types are, what charges to use, and how to index
> the molecule. At  least, thats what the error messages indicate  :>

Sound more like somethings wrong with the topology rather then
the 'UNK' residues.
Please post the error message and a few lines of the coordinate file.

Christoph Freudenberger
Abt. Organische Chemie I AK Siehl - Uni Ulm -Tel: ++49-731-502-2785

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